Stark JM, Hart SC. 1996. Diffusion technique for preparing salt solutions, Kjeldahl digests, and persulfate digests for nitrogen-15 analysis. Soil Science Society of America Journal 60: 1846-1855.
These authors evaluated the recently-developed Teflon-encased-acid-trap technique for collecting nitrogen from water samples for analysis, especially stable isotope (15N) analysis. Earlier acid trap techniques, which rely on the chemistry of ammonium/ammonia in solutions of varying pH, were based on suspended small vials containing acid solutions above a larger volume of sample solution at high pH. Ammonium present in the sample is converted to ammonia by high pH, and escapes solution into the gas phase. It is captured in acid solution; in a closed container with a separate acidic region, ammonium will migrate from the alkaline sample to the acid trap. Suspended trap designs are vulnerable to a number of problems, including vulnerability of the acid trap to contamination by alkaline solution and subsequent loss of captured ammonium. Teflon will pass gases but not liquids, and therefore provides an ideal barrier between the sample and the acid trap that will permit ammonia to enter the trap.
These authors conducted a set of six experiments to evaluate the utility of Teflon acid traps. First, blanks were evaluated, to determine the sensitivity of the technique to nitrogen derived from contamination in the various materials of the experiment (filter paper, Teflon, plastic bottles, etc.). There was some nitrogen detectable from these non-sample sources, but a correction factor could be constructed based on including a few blanks in sample sets. The second experiment examined the recovery of ammonium from 2M KCl solutions. These solutions are very similar to the solutions extracted from soils of Alexandra Fjord in 2009. As might be expected, incubation time correlated with recovery of ammonium; in addition, Teflon traps performed better over shorter incubations (up to about 6 days) than did suspended traps, though the difference disappeared at the longest (8 days) incubations.
The third experiment was of greatest interest to me. They examined the open-bottle time necessary to eliminate residual ammonium from samples used in experiment 2, and the incubation conditions to collect NO3- -derived nitrogen using Devarda’s alloy to reduce NO3- to NH4+. Residual ammonium left in solution at the end of the first reaction would contaminate NO3- examination and lead to overestimation of NO3- contents; this is especially true when the two forms of nitrogen have been previously enriched with 15N to different degrees. There is a trade-off between open bottle time (ranging in these experiments from one to five days) and recovery of NO3- from samples; long open-bottle times appear to lead to an unknown chemical change in samples, which these authors speculate, may involve sorption of atmospheric CO2. Long ammonium-collection times (i.e. experiment 2) do tend to collect the great majority of ammonium present, recovering on average more than 97% of ammonium from known-concentration samples. This suggests to me a long and potentially nitrate-losing open-bottle incubation is not necessary if ammonium collection has proceeded for at least six days. Agitation of samples, in these experiments often once per day, resulted in a strong improvement in nitrogen capture over at least the shorter (24-96 hour) incubations; our use of continuous agitation for seven days therefore seems likely to capture nearly all ammonium present in samples.
Experiments 4 through 6 were of little interest to me, as I am unfamiliar with Kjeldahl digests and persulfate digests and do not plan to use these techniques in my studies. From what I could glean based on my limited knowledge, the Teflon-acid-trap technique appears to work well with Kjeldahl digests and persulfate digests.
Overall, the Teflon-acid-trap technique performed very well, and had significant ease-of-use and contamination-avoiding advantages over earlier methods. One caution put forth by these authors is regarding the H2 gas evolved during Devarda’s alloy incubations; strong build up of gas can cause leaks, potentially allowing NH3 to escape and leading to underestimates of sample nitrate contents. They suggest storing bottles upside-down during such incubations, as leaks will then include sample solution, and leaking bottles can be easily identified.
Complete recovery of nitrogen was not possible on a routine basis using this technique, but 15N isotope ratios do not rely on 100% recovery if ammonium and / or nitrate concentrations have been measured by an independent method, such as the widely-used colorimetric techniques. The two isotopes of nitrogen do not migrate differently between alkaline sample and acid trap, thus even at relatively inefficient recovery rates, isotopic ratios are maintained. Blanks are important, but in general this technique is robust, reliable, and easy to conduct.
Tuesday, April 20, 2010
Thursday, April 15, 2010
Palmer et al. 2010
Palmer K, Drake HL, Horn MA. 2010. Association of novel and highly diverse acid-tolerant denitrifiers with N2O fluxes of an acidic fen. Applied and Enironmental Microbiology 76: 1125-1134.
These authors examined soils from an acidic fen in southern Germany, and discovered novel denitrifiers that are apparently adapted to local conditions and contribute to the cycling of nitrogen within the fen. Methods employed included measurement of soil parameters, microcosms to examine denitrification rates (both total denitrification and net production / consumption of N2O), cell counts of cultured organisms, and phylogenetic analysis using narG and nosZ sequences and RFLP.
These authors examined soils from an acidic fen in southern Germany, and discovered novel denitrifiers that are apparently adapted to local conditions and contribute to the cycling of nitrogen within the fen. Methods employed included measurement of soil parameters, microcosms to examine denitrification rates (both total denitrification and net production / consumption of N2O), cell counts of cultured organisms, and phylogenetic analysis using narG and nosZ sequences and RFLP.
Tuesday, April 6, 2010
Palmer et al. 2009
Palmer K, Drake HL, Horn MA. 2009. Genome-derived criteria for assigning environmental narG and nosZ sequences to operational taxonomic units of nitrate reducers. Applied and Environmental Microbiology 75: 5170-5174.
These authors compared the sequences of narG and nosZ genes to corresponding sequences of 16s rRNA genes, using in-silico analysis of sequences downloaded from GenBank. While similarities above 97% are commonly used for species- or genus-level taxonomic delineation for 16s sequences, this analysis found much lower threshold similarities for such delineation using the structural genes.
This paper is confusing to me. One part of the text appears to contradict itself, when the authors state that the Nar operon in Pseudomonas stutzeri A1501 is putatively alien in origin (i.e. recent horizontal transfer), then go on to state in the same paragraph that it appears unlikely that the Nar operon was horizontally transferred in any species. I may just be misunderstanding the meaning of the term “putatively alien” in regards to a bacterial gene sequence.
A greater puzzle is presented by the list of nosZ sequences. These authors downloaded 85 such sequences, where my own attempts to extract data from GenBank resulted in only 42 unique nosZ sequences. The list in a supplementary table includes several cases of multiple accessions of the same species but of different PD. The paper these clusters of PD-sequences are derived from is Dandie et al. (2007); a quick scan of this paper did not reveal what the distinction “PD” indicates.
These authors compared the sequences of narG and nosZ genes to corresponding sequences of 16s rRNA genes, using in-silico analysis of sequences downloaded from GenBank. While similarities above 97% are commonly used for species- or genus-level taxonomic delineation for 16s sequences, this analysis found much lower threshold similarities for such delineation using the structural genes.
This paper is confusing to me. One part of the text appears to contradict itself, when the authors state that the Nar operon in Pseudomonas stutzeri A1501 is putatively alien in origin (i.e. recent horizontal transfer), then go on to state in the same paragraph that it appears unlikely that the Nar operon was horizontally transferred in any species. I may just be misunderstanding the meaning of the term “putatively alien” in regards to a bacterial gene sequence.
A greater puzzle is presented by the list of nosZ sequences. These authors downloaded 85 such sequences, where my own attempts to extract data from GenBank resulted in only 42 unique nosZ sequences. The list in a supplementary table includes several cases of multiple accessions of the same species but of different PD. The paper these clusters of PD-sequences are derived from is Dandie et al. (2007); a quick scan of this paper did not reveal what the distinction “PD” indicates.
Thursday, April 1, 2010
Tuomivirta et al. 2009
Tuomivirta TT, Yrjälä K, Frize H. 2009. Quantitative PCR of pmoA using a novel reverse primer correlates with potential methane oxidation in Finnish Fen. Research in Microbiology 160: 751-756.
These authors developed novel primers for studying the methanotrophs of Finnish peatland fens. The existing primer pairs widely used to study methanotrophs, based on the gene pmoA, did not consistently amplify useful products in PCR using template DNA from these fens.
The novel primer pair was tested on 114 samples from two Finnish fens, representing the northern and southern peatlands of Finland. While A189f/A682r failed to provide useful products, the new primer A6821r in conjunction with A189f did produce strong bands. In qPCR, these primers produced results correlated with measured methane oxidation potential, further supporting their utility in these systems.
These authors developed novel primers for studying the methanotrophs of Finnish peatland fens. The existing primer pairs widely used to study methanotrophs, based on the gene pmoA, did not consistently amplify useful products in PCR using template DNA from these fens.
The novel primer pair was tested on 114 samples from two Finnish fens, representing the northern and southern peatlands of Finland. While A189f/A682r failed to provide useful products, the new primer A6821r in conjunction with A189f did produce strong bands. In qPCR, these primers produced results correlated with measured methane oxidation potential, further supporting their utility in these systems.
Schmidt et al. 2008
Schmidt SK, Reed SC, Nemergut DR, Grandy AS, Cleveland CC, Weintraub MN, Hill AW, Costellow EK, Meyer AF, Neff JC, Martin AM. 2008. The earliest stages of ecosystem succession in high-elevation (5000 metres above sea level), recently deglaciated soils. Proceedings of the Royal Society of London, Series B 275: 2793-2802.
These authors describe the microbial community and soil parameters of a chronosequence at the foreground of a receding glacier high in the Peruvian Andes. From a combination of aerial photography and previous work at this site, a series of sites of soils of increasing ages from zero to 79 years old was established. No surface plants, even lichens, are present on any of these new soils, and soil nutrient levels (carbon, nitrogen) are very low; the only organisms present are microorganisms.
Two previous hypotheses had been proposed to explain the dynamics of very early primary succession on new soil. Organic matter has been observed to accumulate slowly in new soils; the source of this material is either aeolian deposits (i.e. wind-borne plant detritus and pollen) or in-situ fixation of CO2 and N2. These are not mutually exclusive hypotheses, but the relative contributions of each are explored in this study.
The methods used here cover an extensive list of soil parameters. Three sets of soil samples were collected: for microbiological analysis, N-fixation measurement, and all other chemical analyses. The other chemical analyses include photosynthetic pigment extraction, soil total and mineral nitrogen, pyrolysis for identifying sources of carbon compounds (i.e. microbial-autotroph, microbial-heterotroph, plant), enzyme assays for common and informative microbial enzymes, and soil stability analysis of the resistance of these new soils to erosion forces such as water runoff.
These authors focused on the cyanobacterial fraction of the microbial community in this study; some details of other components of the biota are described in an earlier paper, Nemergut et al. (2007). Cyanobacteria are autotrophs also capable of fixing atmospheric nitrogen, thus they are ideal primary colonizers of new soil as they require little more than a source of moisture and air. Analysis of the community included the use of the P-test (Martin 2002); note that as in Nemergut et al. (2007), he is one of the authors of this study. The analytical approach is very similar to that employed in the earlier study, with a comparison of discovered sequences to published sequences from around the world. In this study, cyanobacterial sequences from zero and 4-year-old soils were similar to sequences from an extremely broad sample of habitats, including Antarctic lake ice, marine subseafloor sediments, urban aerosols, forest soils, and oil-polluted soils.
The soil chronosequence showed a clear pattern of stages of primary succession at every level of analysis. The soil microbial community became both more abundant and more diverse through time, soil nutrients increased, the chemical environment included increasing amounts and diversity of complex organic molecules, key enzyme pathways became established, and soil stability increased as soils aged. N-fixation showed a peak, with increasing N-fixation activity from the zero to 4-year-old soils (by two orders of magnitude), then declining by about half in the 79-year-old soils. This mirrors and precedes a widely-observed pattern in plant primary succession, in which nitrogen-fixing plants are among the first colonizers, but decline in abundance at later stages of succession. Enzyme and organic molecule patterns were consistent with a total absence of heterotrophs in the extremely young soils, increasing occurrence of organisms capable of decomposing plant matter in the 4-year-old soils, and a molecular ecology qualitatively similar to a mature plant-associated soil in the 79-year-old soil.
The list of procedures and level of detail of analysis in this paper is impressive. Many, though certainly not all, of these techniques will be models for my own work, especially in the summer of 2010. The molecular-diversity techniques pioneered by Martin (Martin 2002, Nemergut et al. 2007, this paper) as well as the techniques of analyzing soil pigments and soil nutrients are all very interesting.
These authors describe the microbial community and soil parameters of a chronosequence at the foreground of a receding glacier high in the Peruvian Andes. From a combination of aerial photography and previous work at this site, a series of sites of soils of increasing ages from zero to 79 years old was established. No surface plants, even lichens, are present on any of these new soils, and soil nutrient levels (carbon, nitrogen) are very low; the only organisms present are microorganisms.
Two previous hypotheses had been proposed to explain the dynamics of very early primary succession on new soil. Organic matter has been observed to accumulate slowly in new soils; the source of this material is either aeolian deposits (i.e. wind-borne plant detritus and pollen) or in-situ fixation of CO2 and N2. These are not mutually exclusive hypotheses, but the relative contributions of each are explored in this study.
The methods used here cover an extensive list of soil parameters. Three sets of soil samples were collected: for microbiological analysis, N-fixation measurement, and all other chemical analyses. The other chemical analyses include photosynthetic pigment extraction, soil total and mineral nitrogen, pyrolysis for identifying sources of carbon compounds (i.e. microbial-autotroph, microbial-heterotroph, plant), enzyme assays for common and informative microbial enzymes, and soil stability analysis of the resistance of these new soils to erosion forces such as water runoff.
These authors focused on the cyanobacterial fraction of the microbial community in this study; some details of other components of the biota are described in an earlier paper, Nemergut et al. (2007). Cyanobacteria are autotrophs also capable of fixing atmospheric nitrogen, thus they are ideal primary colonizers of new soil as they require little more than a source of moisture and air. Analysis of the community included the use of the P-test (Martin 2002); note that as in Nemergut et al. (2007), he is one of the authors of this study. The analytical approach is very similar to that employed in the earlier study, with a comparison of discovered sequences to published sequences from around the world. In this study, cyanobacterial sequences from zero and 4-year-old soils were similar to sequences from an extremely broad sample of habitats, including Antarctic lake ice, marine subseafloor sediments, urban aerosols, forest soils, and oil-polluted soils.
The soil chronosequence showed a clear pattern of stages of primary succession at every level of analysis. The soil microbial community became both more abundant and more diverse through time, soil nutrients increased, the chemical environment included increasing amounts and diversity of complex organic molecules, key enzyme pathways became established, and soil stability increased as soils aged. N-fixation showed a peak, with increasing N-fixation activity from the zero to 4-year-old soils (by two orders of magnitude), then declining by about half in the 79-year-old soils. This mirrors and precedes a widely-observed pattern in plant primary succession, in which nitrogen-fixing plants are among the first colonizers, but decline in abundance at later stages of succession. Enzyme and organic molecule patterns were consistent with a total absence of heterotrophs in the extremely young soils, increasing occurrence of organisms capable of decomposing plant matter in the 4-year-old soils, and a molecular ecology qualitatively similar to a mature plant-associated soil in the 79-year-old soil.
The list of procedures and level of detail of analysis in this paper is impressive. Many, though certainly not all, of these techniques will be models for my own work, especially in the summer of 2010. The molecular-diversity techniques pioneered by Martin (Martin 2002, Nemergut et al. 2007, this paper) as well as the techniques of analyzing soil pigments and soil nutrients are all very interesting.
Wednesday, March 31, 2010
Sørensen et al. 2006
Sørensen LI, Holmstrup M, Maraldo K, Christensen S, Christensen B. 2006. Soil fauna communities and microbial respiration in high Arctic tundra soils at Zackenberg, Northeast Greenland. Polar Biology 29: 189-195.
These authors sampled soil animals from three sites at Zackenberg station, Greenland, over three days in mid-summer. Two of the sites were considered mesic heath, with a mix of Cassiope tetragona and other High Arctic species of plants, while the third site was dominated by Dryas spp. and was considered dry heath; snow melts from the dry heath up to 20 days earlier than from the mesic heaths. Soil samples ranging down to about 6cm depth were collected, stored at 5ºC for up to two weeks, and analyzed by a range of methods in the laboratories in Europe.
Different groups of soil animals were extracted by varying methods. Soil microarthropods, a diverse group dominated by Collebola and Acari, were extracted by modified MacFadyen funnels into Benzoic acid. Enchytraeids and dipteran larvae were extracted in Baermann wet funnels with heating of the samples, into tap water. Protozoa were washed from soils in water and grown on media plates in the dark at 10ºC. Nematodes were collected by the Blender-Cotton wool method of Schouten and Arp (1991). Soil microbial respiration was measured in serum bottles, with the CO2 concentration in the headspace measured at zero, 5 and 25 hours, with a fully factorial design of nutrient amendments of C, N, and P. Soil pH and soil organic matter content, but not moisture content or other nutrient concentrations were determined using methods not clearly described, though presumably these procedures were similar to standard methods.
Once abundance and biomass data was collected, comparisons between plots were made using multivariate analysis and a software package named PRIMER 5.0. My understanding is the species counts were (log+1) transformed to reduce the influence of very abundant species, then analyzed using an approach similar to Principal Components Analysis. The result of this analysis was a clear difference between the dry heath and the two mesic heaths, while the two mesic heaths were not different from each other in parameter-space. A Bray-Curtis similarity matrix was also involved, though I’m not certain I understand how.
Different taxonomic groups were identified to different taxonomic levels; 19 species of Collembola and 7 species of Enchytraeids were found, for example, but Acari were identified to suborder (Cryptostigmata (oribatids), Prostigmata, Mesostigmata) and nematodes and protozoans were counted at those high taxonomic levels. While the two mesic heath sites were only marginally significantly different from each other, there was a clear increase in abundances in the dry heath site. For collembola at least, the dry heath site was also dominated by two highly abundant species, which differed from the majority of species in the mesic sites by being unpigmented and associated with sub-surface, rather than soil-surface, regions in the soil. The higher abundance of probably bacteria-eating nematodes at the dry heath strongly suggests higher turnover of microorganisms as well as generally higher biological activity from the higher populations of most soil animals.
These authors suggest higher organic matter decomposition rates at the dry heath, which seems reasonable given the higher animal populations there. However, their attribution of higher soil pH there to higher respiration levels seems like more of a stretch, absent supporting mineralogical and soil-nutrient data.
This paper provides an excellent example of the data that can be collected and analyzed from a brief but intensive study of soil invertebrates at a High Arctic site. In addition, meaningful information about differences in biodiversity between locations can be derived from studies of organisms not identified to fine taxonomic levels.
These authors sampled soil animals from three sites at Zackenberg station, Greenland, over three days in mid-summer. Two of the sites were considered mesic heath, with a mix of Cassiope tetragona and other High Arctic species of plants, while the third site was dominated by Dryas spp. and was considered dry heath; snow melts from the dry heath up to 20 days earlier than from the mesic heaths. Soil samples ranging down to about 6cm depth were collected, stored at 5ºC for up to two weeks, and analyzed by a range of methods in the laboratories in Europe.
Different groups of soil animals were extracted by varying methods. Soil microarthropods, a diverse group dominated by Collebola and Acari, were extracted by modified MacFadyen funnels into Benzoic acid. Enchytraeids and dipteran larvae were extracted in Baermann wet funnels with heating of the samples, into tap water. Protozoa were washed from soils in water and grown on media plates in the dark at 10ºC. Nematodes were collected by the Blender-Cotton wool method of Schouten and Arp (1991). Soil microbial respiration was measured in serum bottles, with the CO2 concentration in the headspace measured at zero, 5 and 25 hours, with a fully factorial design of nutrient amendments of C, N, and P. Soil pH and soil organic matter content, but not moisture content or other nutrient concentrations were determined using methods not clearly described, though presumably these procedures were similar to standard methods.
Once abundance and biomass data was collected, comparisons between plots were made using multivariate analysis and a software package named PRIMER 5.0. My understanding is the species counts were (log+1) transformed to reduce the influence of very abundant species, then analyzed using an approach similar to Principal Components Analysis. The result of this analysis was a clear difference between the dry heath and the two mesic heaths, while the two mesic heaths were not different from each other in parameter-space. A Bray-Curtis similarity matrix was also involved, though I’m not certain I understand how.
Different taxonomic groups were identified to different taxonomic levels; 19 species of Collembola and 7 species of Enchytraeids were found, for example, but Acari were identified to suborder (Cryptostigmata (oribatids), Prostigmata, Mesostigmata) and nematodes and protozoans were counted at those high taxonomic levels. While the two mesic heath sites were only marginally significantly different from each other, there was a clear increase in abundances in the dry heath site. For collembola at least, the dry heath site was also dominated by two highly abundant species, which differed from the majority of species in the mesic sites by being unpigmented and associated with sub-surface, rather than soil-surface, regions in the soil. The higher abundance of probably bacteria-eating nematodes at the dry heath strongly suggests higher turnover of microorganisms as well as generally higher biological activity from the higher populations of most soil animals.
These authors suggest higher organic matter decomposition rates at the dry heath, which seems reasonable given the higher animal populations there. However, their attribution of higher soil pH there to higher respiration levels seems like more of a stretch, absent supporting mineralogical and soil-nutrient data.
This paper provides an excellent example of the data that can be collected and analyzed from a brief but intensive study of soil invertebrates at a High Arctic site. In addition, meaningful information about differences in biodiversity between locations can be derived from studies of organisms not identified to fine taxonomic levels.
O'Neill et al. 2010
O’Neill KP, Godwin HW, Jiménez-Esquilín AE, Battigelli JP. 2010. Reducing the dimensionality of soil microinvertebrate community datasets using Indicator Species Analysis: Implications for ecosystem monitoring and soil management. Soil Biology & Biochemistry 42: 145-154.
These authors used a dataset of soil microarthropods to evaluate a method for identifying indicator species for ecosystem monitoring. The method centres on the Indicator Value (IV) of a species, a number that integrates the degree of uniqueness to a place of a species and the abundance of that species within a given habitat. A high IV value indicates both high information content and a high probability of being sampled. The IV is apparently robust to differences in site number and species absolute abundances, and provides a single value for evaluating observed or expected changes in an ecosystem. Indicator species, furthermore, integrate habitat conditions over their lifespans, in contrast to measures of chemical and physical parameters that capture a snapshot of an ecosystem.
The basic evaluation approach here was to identify indicator species along a clear environmental gradient from meadow to forest in West Virginia. The habitat was divided into three zones, with an edge patch between the open meadows and closed-canopy forest. Near-surface soil cores were collected from each zone every month from April 2004 to April 2005 (n = 180), using the top of the mineral soil as the reference depth. Microarthropods were extracted in a modified Macfadyen funnel with a strong and increasing temperature gradient, into 70% ethanol.
Diversity measures, including Simpson’s and Shannon indices, were based on counts of individuals identified to family level (suborder for Acari). Differences between sites were analyzed by 2-way repeated measures ANOVA and Principle Components Analysis, after rare taxa (those that occurred in less than 10% of samples) were removed; rare taxa are extremely unlikely to be identified as indicator species.
Calculating IV for each taxon, regardless of the taxonomic resolution, provides large advantages in labour time and taxonomic expertise, as many microfauna are very difficult to identify to genus or species. These authors state that enumeration of a single sample required more than 1 hour of a trained taxonomist’s time. In studies such as this one, there are further advantages of IV associated with its robustness in the face of many zero measurements (i.e. taxa absent from samples) and the general messiness of these kinds of datasets. However, the ISA approach is intended for 2-stage studies, where an intensive initial survey identifies indicator species (taxa), and later long-term monitoring ignores other species. For studies specificially designed to address biodiversity, such as my own, excluding rare taxa would not be beneficial, and there may be no easy escape from time-consuming morphotaxa sorting.
I have spoken with Dr. Battigelli, the trained taxonomist in this study. He has indicated that while this IV-based approach may not be appropriate for my own work, it nonetheless demonstrates the types of analyses that can be conducted with soil invertebrates identified to middle taxonomic levels. He has assured me I could probably be trained to identify Collembola to Family and Acari to Suborder in a matter of a few days, and he would be interested in futher studies of collected soil invertebrates based on interesting patterns that emerge at these taxonomic levels.
These authors used a dataset of soil microarthropods to evaluate a method for identifying indicator species for ecosystem monitoring. The method centres on the Indicator Value (IV) of a species, a number that integrates the degree of uniqueness to a place of a species and the abundance of that species within a given habitat. A high IV value indicates both high information content and a high probability of being sampled. The IV is apparently robust to differences in site number and species absolute abundances, and provides a single value for evaluating observed or expected changes in an ecosystem. Indicator species, furthermore, integrate habitat conditions over their lifespans, in contrast to measures of chemical and physical parameters that capture a snapshot of an ecosystem.
The basic evaluation approach here was to identify indicator species along a clear environmental gradient from meadow to forest in West Virginia. The habitat was divided into three zones, with an edge patch between the open meadows and closed-canopy forest. Near-surface soil cores were collected from each zone every month from April 2004 to April 2005 (n = 180), using the top of the mineral soil as the reference depth. Microarthropods were extracted in a modified Macfadyen funnel with a strong and increasing temperature gradient, into 70% ethanol.
Diversity measures, including Simpson’s and Shannon indices, were based on counts of individuals identified to family level (suborder for Acari). Differences between sites were analyzed by 2-way repeated measures ANOVA and Principle Components Analysis, after rare taxa (those that occurred in less than 10% of samples) were removed; rare taxa are extremely unlikely to be identified as indicator species.
Calculating IV for each taxon, regardless of the taxonomic resolution, provides large advantages in labour time and taxonomic expertise, as many microfauna are very difficult to identify to genus or species. These authors state that enumeration of a single sample required more than 1 hour of a trained taxonomist’s time. In studies such as this one, there are further advantages of IV associated with its robustness in the face of many zero measurements (i.e. taxa absent from samples) and the general messiness of these kinds of datasets. However, the ISA approach is intended for 2-stage studies, where an intensive initial survey identifies indicator species (taxa), and later long-term monitoring ignores other species. For studies specificially designed to address biodiversity, such as my own, excluding rare taxa would not be beneficial, and there may be no easy escape from time-consuming morphotaxa sorting.
I have spoken with Dr. Battigelli, the trained taxonomist in this study. He has indicated that while this IV-based approach may not be appropriate for my own work, it nonetheless demonstrates the types of analyses that can be conducted with soil invertebrates identified to middle taxonomic levels. He has assured me I could probably be trained to identify Collembola to Family and Acari to Suborder in a matter of a few days, and he would be interested in futher studies of collected soil invertebrates based on interesting patterns that emerge at these taxonomic levels.
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